CNA prediction clashing with cell type annotation

[Aditya-Gautam20]

Hello CopyKAT team,

Thank you for developing and maintaining this tool. I ran CopyKAT on my single-cell dataset and generated an aneuploid/diploid/not.defined table across cell types. Surprisingly, many immune cells (e.g., B cells, T cells, Myeloid cells) are classified as aneuploid in my adata.

Could you please advise why this might occur? Are there known scenarios where immune cells are flagged as aneuploid, or is this likely due to technical or parameter issues in CopyKAT or the data?

Thank you.